2-D to 3-D Refinement of Post Mortem Optical and MRI Co-registration. In: Ellis RE, Peters TM, editors. Medical Image Computing and Computer-Assisted Intervention - MICCAI 2003. Berlin: Springer Berlin Heidelberg; 2003. pp. 935-44. [DOI: 10.1007/978-3-540-39903-2_114]

Structure-Based Intensity Propagation for 3-D Brain Reconstruction With Multilayer Section Microscopy

Microscopy is widely used for brain research because of its high resolution and ability to stain for many different biomarkers. Since whole brains are usually sectioned for tissue staining and imaging, reconstruction of 3D brain volumes from these sections is important for visualization and analysis. Recently developed tissue clearing techniques and advanced confocal microscopy enable multilayer sections to be imaged without compromising the resolution. However, noticeable structure inconsistence occurs if surface layers are used to align these sections. In this paper, a structure-based intensity propagation method is designed for the robust representation of multilayer sections. The 3D structures in reconstructed brains are more consistent using the proposed methods. Experiments are conducted on 367 multilayer sections from 20 mouse brains. The average reconstruction quality measured by the structure consistence index increases by 45% with the tissue flattening method and 29% further with the structure-based intensity propagation.

Automatic quantification of changes in bone in serial MR images of joints

Recent innovations in drug therapies have made it highly desirable to obtain sensitive biomarkers of disease progression that can be used to quantify the performance of candidate disease modifying drugs. In order to measure potential image-based biomarkers of disease progression in an experimental model of rheumatoid arthritis (RA), we present two different methods to automatically quantify changes in a bone in in-vivo serial magnetic resonance (MR) images from the model. Both methods are based on rigid and nonrigid image registration to perform the analysis. The first method uses segmentation propagation to delineate a bone from the serial MR images giving a global measure of temporal changes in bone volume. The second method uses rigid body registration to determine intensity change within a bone, and then maps these into a reference coordinate system using nonrigid registration. This gives a local measure of temporal changes in bone lesion volume. We detected significant temporal changes in local bone lesion volume in five out of eight identified candidate bone lesion regions, and significant difference in local bone lesion volume between male and female subjects in three out of eight candidate bone lesion regions. But the global bone volume was found to be fluctuating over time. Finally, we compare our findings with histology of the subjects and the manual segmentation of bone lesions.

The creation of a brain atlas for image guided neurosurgery using serial histological data

Digital and print brain atlases have been used with success to help in the planning of neurosurgical interventions. In this paper, a technique presented for the creation of a brain atlas of the basal ganglia and the thalamus derived from serial histological data. Photographs of coronal histological sections were digitized and anatomical structures were manually segmented. A slice-to-slice nonlinear registration technique was used to correct for spatial distortions introduced into the histological data set at the time of acquisition. Since the histological data were acquired without any anatomical reference (e.g., block-face imaging, post-mortem MRI), this registration technique was optimized to use an error metric which calculates a nonlinear transformation minimizing the mean distance between the segmented contours between adjacent pairs of slices in the data set. A voxel-by-voxel intensity correction field was also estimated for each slice to correct for lighting and staining inhomogeneity. The reconstructed three-dimensional (3D) histological volume can be viewed in transverse and sagittal directions in addition to the original coronal. Nonlinear transformations used to correct for spatial distortions of the histological data were applied to the segmented structure contours. These contours were then tessellated to create three-dimensional geometric objects representing the different anatomic regions in register with the histological volumes. This yields two alternate representations (one histological and one geometric) of the atlas. To register the atlas to a standard reference MR volume created from the average of 27 T1-weighted MR volumes, a pseudo-MRI was created by setting the intensity of each anatomical region defined in the geometric atlas to match the intensity of the corresponding region of the reference MR volume. This allowed the estimation of a 3D nonlinear transformation using a correlation based registration scheme to fit the atlas to the reference MRI. The result of this procedure is a contiguous 3D histological volume, a set of 3D objects defining the basal ganglia and thalamus, both of which are registered to a standard MRI data set, for use for neurosurgical planning.